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- PDB-4a4e: Solution structure of SMN Tudor domain in complex with symmetrica... -

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Basic information

Entry
Database: PDB / ID: 4a4e
TitleSolution structure of SMN Tudor domain in complex with symmetrically dimethylated arginine
ComponentsSURVIVAL MOTOR NEURON PROTEIN
KeywordsRNA BINDING PROTEIN
Function / homology
Function and homology information


Gemini of coiled bodies / SMN complex / SMN-Sm protein complex / spliceosomal complex assembly / spliceosomal snRNP assembly / Cajal body / DNA-templated transcription termination / Z disc / cytoplasmic ribonucleoprotein granule / nervous system development ...Gemini of coiled bodies / SMN complex / SMN-Sm protein complex / spliceosomal complex assembly / spliceosomal snRNP assembly / Cajal body / DNA-templated transcription termination / Z disc / cytoplasmic ribonucleoprotein granule / nervous system development / snRNP Assembly / SARS-CoV-2 modulates host translation machinery / perikaryon / nuclear body / neuron projection / axon / RNA binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / : / Survival Motor Neuron, YG-box / Survival Motor Neuron, Gemin2-binding domain / SMN complex subunit Smn1 / : / Survival motor neuron, Tudor domain / Survival motor neuron protein (SMN), Tudor domain / Tudor domain profile. / Tudor domain ...: / : / Survival Motor Neuron, YG-box / Survival Motor Neuron, Gemin2-binding domain / SMN complex subunit Smn1 / : / Survival motor neuron, Tudor domain / Survival motor neuron protein (SMN), Tudor domain / Tudor domain profile. / Tudor domain / Tudor domain / SH3 type barrels. - #140 / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
N3, N4-DIMETHYLARGININE / Survival motor neuron protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / simulated annealing
AuthorsTripsianes, K. / Madl, T. / Machyna, M. / Fessas, D. / Englbrecht, C. / Fischer, U. / Neugebauer, K.M. / Sattler, M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Structural Basis for Dimethyl-Arginine Recognition by the Tudor Domains of Human Smn and Spf30 Proteins
Authors: Tripsianes, K. / Madl, T. / Machyna, M. / Fessas, D. / Englbrecht, C. / Fischer, U. / Neugebauer, K.M. / Sattler, M.
History
DepositionOct 12, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2011Group: Database references
Revision 1.2Dec 28, 2011Group: Other
Revision 1.3Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SURVIVAL MOTOR NEURON PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,2962
Polymers7,0941
Non-polymers2021
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200LOWEST ENERGY
RepresentativeModel #1

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Components

#1: Protein SURVIVAL MOTOR NEURON PROTEIN / SURVIVAL MOTOR NEURON PROTEIN SMN / COMPONENT OF GEMS 1 / GEMIN-1


Mass: 7093.893 Da / Num. of mol.: 1 / Fragment: TUDOR DOMAIN, RESIDUES 84-147
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q16637
#2: Chemical ChemComp-2MR / N3, N4-DIMETHYLARGININE


Type: L-peptide linking / Mass: 202.254 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N4O2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N-EDITED 3D NOESY
221F1 15N/13C FILTERED
23115N- EDITED 3D NOESY
34113C- EDITED 3D NOESY (ALIPHATICS)
451F1 15N/13C FILTERED
46113C-EDITED 3D NOESY (ALIPHATICS)
57113C- EDITED 3D NOESY (AROMATICS)
681F1 15N/13C FILTERED
69113C-EDITED 3D NOESY (AROMATICS)
NMR detailsText: NONE

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Sample preparation

DetailsContents: 93% WATER/7% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150 mM6.51.0 atm298.0 K
250 mM6.51.0 atm298.0 K
350 mM6.51.0 atm298.0 K
450 mM6.51.0 atm298.0 K
550 mM6.51.0 atm298.0 K
650 mM6.51.0 atm298.0 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 750 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE,SIMONSON,WARRENrefinement
TALOSstructure solution
CYANAstructure solution
CNSstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 200 / Conformers submitted total number: 20

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